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Fluorine in PDB 4koe: Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae

Enzymatic activity of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae

All present enzymatic activity of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae:
5.99.1.3;

Protein crystallography data

The structure of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 4koe was solved by I.Laponogov, X.-S.Pan, D.A.Veselkov, L.M.Fisher, M.R.Sanderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.42 / 3.02
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.040, 158.040, 210.420, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 21

Other elements in 4koe:

The structure of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae (pdb code 4koe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 4koe:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4koe

Go back to Fluorine Binding Sites List in 4koe
Fluorine binding site 1 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:77.2
occ:1.00
 F04 F:TR6101 0.0 77.2 1.0
C03 F:TR6101 1.3 78.8 1.0
C05 F:TR6101 2.3 82.0 1.0
C02 F:TR6101 2.3 73.5 1.0
H051 F:TR6101 2.5 98.4 1.0
H021 F:TR6101 2.6 88.2 1.0
CA C:ARG456 3.3 67.6 1.0
CB C:ARG456 3.6 61.0 1.0
C06 F:TR6101 3.6 84.1 1.0
C01 F:TR6101 3.6 78.5 1.0
N C:GLY457 3.7 85.8 1.0
C C:ARG456 3.7 79.2 1.0
OD2 C:ASP435 3.9 0.4 1.0
O5' H:DG1 3.9 0.7 1.0
OP1 H:DG1 3.9 0.7 1.0
N C:ASP435 4.0 80.5 1.0
CA C:GLY434 4.0 68.7 1.0
O C:LEU455 4.1 71.9 1.0
C08 F:TR6101 4.1 83.0 1.0
P H:DG1 4.3 0.8 1.0
H011 F:TR6101 4.4 94.2 1.0
N C:ARG456 4.4 70.3 1.0
C C:GLY434 4.5 70.3 1.0
OP2 H:DG1 4.6 0.2 1.0
C C:LEU455 4.7 73.7 1.0
F07 F:TR6101 4.7 77.9 1.0
O C:ARG456 4.7 82.8 1.0
C4' H:DG1 4.7 1.0 1.0
CA C:GLY457 4.7 78.6 1.0
CG C:ASP435 4.8 0.4 1.0
C5' H:DG1 4.8 0.2 1.0
N C:GLY434 4.9 70.9 1.0
CB C:ASP435 4.9 83.6 1.0
O4' H:DG1 4.9 0.7 1.0

Fluorine binding site 2 out of 6 in 4koe

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Fluorine binding site 2 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:77.9
occ:1.00
 F07 F:TR6101 0.0 77.9 1.0
C06 F:TR6101 1.3 84.1 1.0
C05 F:TR6101 2.3 82.0 1.0
C08 F:TR6101 2.4 83.0 1.0
H051 F:TR6101 2.5 98.4 1.0
N09 F:TR6101 2.9 77.7 1.0
H251 F:TR6101 2.9 87.2 1.0
N1 E:DT15 2.9 63.2 1.0
C2 E:DT15 2.9 66.4 1.0
C25 F:TR6101 3.1 72.6 1.0
C6 E:DT15 3.1 67.0 1.0
N3 E:DT15 3.2 59.3 1.0
C2' E:DT15 3.2 60.5 1.0
O2 E:DT15 3.4 73.4 1.0
C5 E:DT15 3.5 66.5 1.0
C4 E:DT15 3.5 71.8 1.0
C1' E:DT15 3.5 63.1 1.0
C03 F:TR6101 3.6 78.8 1.0
C01 F:TR6101 3.6 78.5 1.0
C10 F:TR6101 3.8 75.5 1.0
C02 F:TR6101 4.1 73.5 1.0
C24 F:TR6101 4.2 86.2 1.0
O4 E:DT15 4.3 73.0 1.0
N11 F:TR6101 4.3 77.7 1.0
H011 F:TR6101 4.4 94.2 1.0
C7 E:DT15 4.5 73.8 1.0
CA C:GLY457 4.5 78.6 1.0
OP1 H:DG1 4.6 0.7 1.0
F04 F:TR6101 4.7 77.2 1.0
C3' E:DT15 4.7 71.8 1.0
O5' H:DG1 4.7 0.7 1.0
O4' E:DT15 4.8 69.3 1.0
C22 F:TR6101 4.8 73.4 1.0
O28 F:TR6101 4.8 75.3 1.0
N C:GLY457 4.9 85.8 1.0
N1 F:DA5 4.9 79.7 1.0
C23 F:TR6101 5.0 83.1 1.0

Fluorine binding site 3 out of 6 in 4koe

Go back to Fluorine Binding Sites List in 4koe
Fluorine binding site 3 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:66.2
occ:1.00
 F30 F:TR6101 0.0 66.2 1.0
C20 F:TR6101 1.3 70.4 1.0
C12 F:TR6101 2.3 74.9 1.0
C21 F:TR6101 2.4 74.7 1.0
H211 F:TR6101 2.6 89.6 1.0
H191 F:TR6101 2.7 90.4 1.0
N13 F:TR6101 2.7 76.5 1.0
C2 F:DC4 2.9 86.5 1.0
C19 F:TR6101 3.0 75.3 1.0
N1 F:DC4 3.1 92.7 1.0
N3 F:DC4 3.1 82.4 1.0
H192 F:TR6101 3.1 90.4 1.0
N7 F:DA5 3.2 70.9 1.0
C6 F:DC4 3.3 94.7 1.0
C4 F:DC4 3.3 77.4 1.0
C5 F:DA5 3.3 75.9 1.0
C5 F:DC4 3.4 78.9 1.0
O2 F:DC4 3.5 93.8 1.0
N11 F:TR6101 3.5 77.7 1.0
C8 F:DA5 3.6 75.2 1.0
C22 F:TR6101 3.6 73.4 1.0
C6 F:DA5 3.8 72.1 1.0
C1' F:DC4 3.8 0.2 1.0
C4 F:DA5 3.9 77.4 1.0
C2' F:DC4 4.0 94.2 1.0
N9 F:DA5 4.0 77.0 1.0
C10 F:TR6101 4.1 75.5 1.0
N6 F:DA5 4.1 63.7 1.0
C14 F:TR6101 4.1 79.1 1.0
N4 F:DC4 4.1 78.6 1.0
C18 F:TR6101 4.4 76.2 1.0
H142 F:TR6101 4.4 95.0 1.0
H141 F:TR6101 4.5 95.0 1.0
N1 H:DG1 4.5 0.9 1.0
H161 F:TR6101 4.5 0.0 1.0
N2 H:DG1 4.6 0.6 1.0
N1 F:DA5 4.6 79.7 1.0
N3 F:DA5 4.7 85.0 1.0
C23 F:TR6101 4.8 83.1 1.0
O4' F:DA5 4.8 86.8 1.0
C2 F:DA5 4.9 86.5 1.0
C2 H:DG1 4.9 0.5 1.0
C15 F:TR6101 4.9 84.3 1.0
O29 F:TR6101 5.0 90.2 1.0
C16 F:TR6101 5.0 84.1 1.0

Fluorine binding site 4 out of 6 in 4koe

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Fluorine binding site 4 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:63.5
occ:1.00
 F04 H:TR6101 0.0 63.5 1.0
C03 H:TR6101 1.3 68.0 1.0
C05 H:TR6101 2.3 80.0 1.0
C02 H:TR6101 2.3 61.1 1.0
H051 H:TR6101 2.5 96.0 1.0
H021 H:TR6101 2.6 73.1 1.0
CA D:ARG456 3.3 71.7 1.0
C06 H:TR6101 3.6 77.1 1.0
C01 H:TR6101 3.6 71.7 1.0
N D:GLY457 3.6 85.8 1.0
OP1 F:DA1 3.7 0.3 1.0
CB D:ARG456 3.7 80.4 1.0
OD2 D:ASP435 3.8 0.1 1.0
CA D:GLY434 3.8 75.8 1.0
N D:ASP435 3.9 81.7 1.0
C D:ARG456 3.9 85.2 1.0
O5' F:DA1 3.9 0.5 1.0
O D:LEU455 4.1 86.0 1.0
C08 H:TR6101 4.1 71.1 1.0
CG D:ARG456 4.2 59.8 1.0
P F:DA1 4.2 1.0 1.0
C D:GLY434 4.3 74.6 1.0
H011 H:TR6101 4.4 86.0 1.0
N D:ARG456 4.4 70.1 1.0
OP2 F:DA1 4.6 0.4 1.0
CG D:ASP435 4.6 0.1 1.0
F07 H:TR6101 4.7 63.8 1.0
C D:LEU455 4.7 75.7 1.0
N D:GLY434 4.7 79.0 1.0
C4' F:DA1 4.7 0.9 1.0
C5' F:DA1 4.8 0.6 1.0
CA D:GLY457 4.8 84.3 1.0
CB D:ASP435 4.9 84.4 1.0
H141 H:TR6101 4.9 78.8 1.0
CA D:ASP435 5.0 75.2 1.0

Fluorine binding site 5 out of 6 in 4koe

Go back to Fluorine Binding Sites List in 4koe
Fluorine binding site 5 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:63.8
occ:1.00
 F07 H:TR6101 0.0 63.8 1.0
C06 H:TR6101 1.3 77.1 1.0
C05 H:TR6101 2.3 80.0 1.0
C08 H:TR6101 2.4 71.1 1.0
H051 H:TR6101 2.5 96.0 1.0
N09 H:TR6101 2.8 70.9 1.0
C2 G:DT15 2.8 68.3 1.0
N1 G:DT15 2.9 60.6 1.0
H251 H:TR6101 2.9 78.4 1.0
N3 G:DT15 3.0 64.5 1.0
C25 H:TR6101 3.1 65.5 1.0
C2' G:DT15 3.2 61.0 1.0
C6 G:DT15 3.3 58.7 1.0
O2 G:DT15 3.3 71.1 1.0
C4 G:DT15 3.4 65.7 1.0
C5 G:DT15 3.5 64.2 1.0
C1' G:DT15 3.6 62.0 1.0
C03 H:TR6101 3.6 68.0 1.0
C01 H:TR6101 3.6 71.7 1.0
C10 H:TR6101 3.7 77.5 1.0
C02 H:TR6101 4.1 61.1 1.0
N11 H:TR6101 4.2 74.5 1.0
C24 H:TR6101 4.2 82.3 1.0
O4 G:DT15 4.3 58.9 1.0
CA D:GLY457 4.4 84.3 1.0
H011 H:TR6101 4.4 86.0 1.0
C3' G:DT15 4.5 72.8 1.0
OP1 F:DA1 4.6 0.3 1.0
C7 G:DT15 4.6 68.4 1.0
F04 H:TR6101 4.7 63.5 1.0
C22 H:TR6101 4.7 84.7 1.0
N D:GLY457 4.7 85.8 1.0
O4' G:DT15 4.8 62.1 1.0
O27 H:TR6101 4.8 73.3 1.0
N1 H:DA5 4.8 79.9 1.0
H141 H:TR6101 4.8 78.8 1.0
C23 H:TR6101 4.9 81.1 1.0
O5' F:DA1 5.0 0.5 1.0

Fluorine binding site 6 out of 6 in 4koe

Go back to Fluorine Binding Sites List in 4koe
Fluorine binding site 6 out of 6 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:78.0
occ:1.00
 F30 H:TR6101 0.0 78.0 1.0
C20 H:TR6101 1.3 67.2 1.0
C12 H:TR6101 2.3 72.8 1.0
C21 H:TR6101 2.4 92.0 1.0
H211 H:TR6101 2.6 0.5 1.0
N13 H:TR6101 2.7 69.3 1.0
H191 H:TR6101 2.8 81.7 1.0
H192 H:TR6101 2.8 81.7 1.0
C2 H:DT4 2.9 94.4 1.0
C19 H:TR6101 2.9 68.1 1.0
N3 H:DT4 3.0 94.4 1.0
N1 H:DT4 3.0 0.9 1.0
N7 H:DA5 3.1 66.8 1.0
C5 H:DA5 3.2 70.5 1.0
C6 H:DT4 3.3 0.4 1.0
C4 H:DT4 3.4 92.4 1.0
O2 H:DT4 3.4 88.9 1.0
C5 H:DT4 3.5 0.4 1.0
C8 H:DA5 3.5 78.8 1.0
N11 H:TR6101 3.5 74.5 1.0
C22 H:TR6101 3.6 84.7 1.0
C6 H:DA5 3.7 71.0 1.0
C1' H:DT4 3.8 1.0 1.0
C4 H:DA5 3.8 66.7 1.0
C2' H:DT4 3.9 0.2 1.0
N6 H:DA5 3.9 65.0 1.0
N9 H:DA5 4.0 74.6 1.0
C10 H:TR6101 4.1 77.5 1.0
C14 H:TR6101 4.1 65.6 1.0
O4 H:DT4 4.2 84.1 1.0
C18 H:TR6101 4.4 72.3 1.0
H142 H:TR6101 4.5 78.8 1.0
N1 H:DA5 4.5 79.9 1.0
H141 H:TR6101 4.5 78.8 1.0
N1 F:DA1 4.5 0.0 1.0
C7 H:DT4 4.6 0.3 1.0
N3 H:DA5 4.7 72.9 1.0
H161 H:TR6101 4.8 86.7 1.0
C23 H:TR6101 4.8 81.1 1.0
O4' H:DA5 4.8 79.5 1.0
C2 H:DA5 4.8 84.7 1.0
C15 H:TR6101 5.0 69.2 1.0
C2 F:DA1 5.0 0.4 1.0

Reference:

I.Laponogov, X.-S.Pan, D.A.Veselkov, L.M.Fisher, M.R.Sanderson. Inhibitor-Stabilised Cleavage Complexes of Topoisomerase Iia: Structural Analysis of Drug-Dependent Inter- and Intramolecular Interactions To Be Published.
Page generated: Thu Aug 1 03:16:12 2024

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